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000277719 041__ $$aEnglish
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000277719 1001_ $$0P:(DE-2719)2814183$$aPollak, Clemens$$b0$$eFirst author$$udzne
000277719 245__ $$aFastSurfer-LIT: Lesion inpainting tool for whole-brain MRI segmentation with tumors, cavities, and abnormalities.
000277719 260__ $$aCambridge, MA$$bMIT Press$$c2025
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000277719 520__ $$aResection cavities, tumors, and other lesions can fundamentally alter brain structure and present as abnormalities in brain MRI. Specifically, quantifying subtle neuroanatomical changes in other, not directly affected regions of the brain is essential to assess the impact of tumors, surgery, chemo/radiotherapy, or drug treatments. However, only a limited number of solutions address this important task, while many standard analysis pipelines simply do not support abnormal brain images at all. In this paper, we present a method to perform sensitive neuroanatomical analysis of healthy brain regions in the presence of large lesions and cavities. Our approach called 'FastSurfer Lesion Inpainting Tool' (FastSurfer-LIT) leverages the recently emerged Denoising Diffusion Probabilistic Models (DDPM) to fill lesion areas with healthy tissue that matches and extends the surrounding tissue. This enables subsequent processing with established MRI analysis methods such as the calculation of adjusted volume and surface measurements using FastSurfer or FreeSurfer. FastSurfer-LIT significantly outperforms previously proposed solutions on a large dataset of simulated brain tumors (N = 100) and synthetic multiple sclerosis lesions (N = 39) with improved Dice and Hausdorff measures, and also on a highly heterogeneous dataset with lesions and cavities in a manual assessment (N = 100). Finally, we demonstrate increased reliability to reproduce pre-operative cortical thickness estimates from corresponding post-operative temporo-mesial resection surgery MRIs. The method is publicly available at https://github.com/Deep-MI/LIT and will be integrated into the FastSurfer toolbox.
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000277719 7001_ $$0P:(DE-2719)2814290$$aKügler, David$$b1$$udzne
000277719 7001_ $$0P:(DE-2719)9002598$$aBauer, Tobias$$b2$$udzne
000277719 7001_ $$aRüber, Theodor$$b3
000277719 7001_ $$0P:(DE-2719)2812134$$aReuter, Martin$$b4$$eLast author$$udzne
000277719 773__ $$0PERI:(DE-600)3167925-0$$a10.1162/imag_a_00446$$gVol. 3, p. imag_a_00446$$pimag_a_00446$$tImaging neuroscience$$v3$$x2837-6056$$y2025
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000277719 9141_ $$y2025
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